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bioRxiv · 10.1101/273656

Assessment and refinement of sample preparation methods for deep and quantitative plant proteome profiling

Song, G.·Hsu, P. Y.·Walley, J. W.
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Abstract

A major challenge in the field of proteomics is obtaining high quality peptides for comprehensive proteome profiling by liquid chromatography mass spectrometry for many organisms. Here we evaluate and modify a range of sample preparation methods using photosynthetically active Arabidopsis leaf tissues from several developmental timepoints. We find that inclusion of FASP-based on filter digestion improves all protein extraction methods tested. Ultimately, we show that a detergent-free urea-FASP approach enables deep and robust quantification of leaf proteomes. For example, from 4-day-old leaf tissue we profiled up to 11,690 proteins from a single sample replicate. This method should be broadly applicable to researchers working on difficult to process samples from a range of plant and non-plant organisms.\n\nAbbreviations

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Song, G., Hsu, P. Y., Walley, J. W.. 2018-02-28. Assessment and refinement of sample preparation methods for deep and quantitative plant proteome profiling. https://doi.org/10.1101/273656

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